Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
6961307 | Advances in Engineering Software | 2018 | 14 Pages |
Abstract
In this paper, we present an optimization strategy for agent-based simulations of biological dynamics using Intel Xeon Phi coprocessors, demonstrated by a prize-winning entry of the “Intel Modern Code Developer Challenge” competition. These optimizations allow simulating various biological mechanisms, in particular the simulation of millions of cells, their proliferation, movements and interactions in 3D space. Overall, our results demonstrate a powerful approach to implement and conduct very detailed and large-scale computational simulations for biological research. We also highlight the main difficulties faced when developing such optimizations, in particular the assessment of the simulation accuracy, the dependencies between different optimization techniques and counter-intuitive effects in the speed of the optimized solution. The overall speedup of 595â¯Ã⯠shows a good parallel scalability.
Keywords
Related Topics
Physical Sciences and Engineering
Computer Science
Software
Authors
Pablo Gonzalez-de-Aledo, Andrey Vladimirov, Marco Manca, Jerry Baugh, Ryo Asai, Marcus Kaiser, Roman Bauer,